In 1962, Josephson made a celebrated prediction: when a constant voltage is applied across a thin insulator separating two superconductors, it will generate an oscillating current(1). These oscillations are ubiquitous in superconducting weak links of various geometries, and analogues have been found in other macroscopic quantum systems, such as superfluids2-4 and gaseous Bose- Einstein condensates(5). The interplay between the oscillating current and external microwave radiation of matching frequency ( Shapiro steps(6)) or with internal electrodynamic resonances (Fiske effect(7)) appear as changes in the current-voltage characteristics of superconducting tunnel junctions and provide further insight into the phenomenon. Here, we report measurements and theoretical studies suggesting that Josephson current oscillations interact with atomic-scale mechanical motion as well. We formed a niobium dimer nanowire that acts as a weak link between two superconducting (bulk) niobium electrodes(8). We find features in the differential conductance through the dimer which we believe correspond to excitations of the dimer vibrational modes by Josephson oscillations and support our results with theoretical simulations.